If you want threatened species for small aquaria, fish are somewhat a mixed blessing. Great because there is an enormously diverse range of species to choose from, sad because so many of them are threatened with extinction. Just some threatened fishes, both fresh and saltwater, that would work in smaller aquaria include:
Extinct in the Wild
Potosi pupfish (Cyprinodon alvarezi), golden skiffia (Skiffia francesae)
Critically Endangered
Red-tailed black shark (Epalzeorhynchos bicolor), coral red pencilfish (Nannostomus mortenthaleri), Japanese rosy bitterling (Rhodeus smithii), dwarf pygmy goby (Pandaka pygmaea), European eel (Anguilla anguilla), spotted handfish (Brachionichthys hirsutus)
Endangered
Blaasop beauty puffer (Chelonodon pleurospilus), Boeseman's rainbowfish (Melanotaenia boesemani), zebra loach (Botia striata), Bangaii cardinalfish (Pterapogon kauderni), red-lined torpedo barb (Sahyadria denisonii)
Vulnerable
Mbam killifish (Aphyosemion dargei), Rohan's barb (Dawkinsia rohani), brick seamoth (Pegasus laternarius), Brunei beauty fighting fish (Betta macrostoma), clarion angelfish (Holacanthus clarionensis), European mudminnow (Umbra krameri), spiny seahorse (Hippocampus histrix), Amur stickleback (Pungitius sinensis)
Near Threatened
Blue-eyed pleco (Panaque cochliodon), chevron butterflyfish (Chaetodon trifascialis), reedfish (Erpetoichthys calabaricus), least rasbora (Boraras urophthalmoides)